In a fuel injection system having a fuel injection pump of distribution type with an electromagnetic valve controlling the communication between a spill port and a lower pressure fuel chamber, the closing duration of the electromagnetic valve is controlled by a computer so that the closing duration is defined as the sum of prestroke time and actual injection time which are both prestored in one or more memories. The actual injection time is controlled in accordance with engine operating condition, while the prestroke time may also be controlled by manually setting the same or by way of a feedback control. The sum, which defines the closing duration of the electromagnetic valve, may be limited by a maximum value, which may be manually adjustable, so as to prevent excessive fuel flow. The prestroke time may be uniformly controlled through all the cylinders or may be independently controlled for respective cylinders.